Over the years roles in regulating plant growth and development have been proposed for numerous classes of chemicals . In evaluating these putative regulatory molecules plant biologists have encountered a number of challenges including the problem of quantifying substances present at trace levels in extremely complex mixtures, the difficulty in obtaining and interpreting phenotypic responses to exogenous applications, and until recently, the inability to selectively alter endogenous levels of these substances. Melatonin is one of the latest potential regulatory molecules identified in plants. Although no specific phenotype is currently associated with this class of chemicals (methoxylated indoleamines) in higher plants, it has important and unique biological activity in many other taxa, from algae to humans. In these organisms, melatonin acts as a night signal, coordinating responses to diurnal and photoperiodic environmental cues. In this article we assess the process by which melatonin has been evaluated in plants so far and find that many of the methods for melatonin analysis, which have been adopted from animal studies, are inappropriate for use with plant materials. Thus despite some interesting preliminary reports, the case for melatonin as a plant regulator is still at an early stage of development.